RetrogeneDB ID: retro_shar_562

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849910.1:218718..219296(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000016712
• Aliases: None
• Description: None

Sequence

>retro_shar_562
GTAGGTCCTTATGTAGATGCTTTAGCAGAGATTAATTACCCTTTGACAGCATATGAACACATTTCTTCTGCTGGTATCAA
AGCATGGGGCACCCTCCCAGGAAAACAATATAGAGGGATAGCCTTCACAAAAATAGCACATGATCCAAATGAACCCTTTG
CTTATTTTGTGGGACATTTGCAGACAGCTGTCATATGAGCTATTGATAAAAATGCACCAACAAGAATTATGATAAGGCAA
CTTGCTAGAGAAAAATCTAGTTTTGTACAAGAGTTATACTAGGACTACACAAGGATGCTCCTTTAGAGGAGATCATAAGA
CACTGTGCCACAGTGGGCACAAATACCTTTTAAAGCCAGGCTATGATGCAGACTTTCCAAGATCCGAACATGGGAAGACA
GGGTTCCTTTTGGCAAAGGACTTCCAGAGAGACTCATCAATGCTTTCAATGTGGTAAAATAGGGCATCTGAAAGCTCAAT
GTTGGCATAAAGGCAGAGTGAAAAAACAGGGTGGGAGAACAAGACCTAAAAACCCCATGTCCAAAATGCAAAATGTCCAG
AGGCTTCCATTGCGCATT

Alignment

ORF - retro_shar_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.22 %
• Parental protein coverage: 61.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGSYVDTSAQINNPIAAYEQIASAAIKAWGFSPGKQGRREAFTKIAQGPNESFADFVGRLQTAVIMNYDE
          VG.YVD..A.IN.P..AYE.I.SA.IKAWG..PGKQ.R..AFTKIA..PNE.FA.FVG.LQTAVI...D.
Retrocopy VGPYVDALAEINYPLTAYEHISSAGIKAWGTLPGKQYRGIAFTKIAHDPNEPFAYFVGHLQTAVI*AIDK

Parental  NAATEIMIRQLVKNANE-VCRRIILGLYKDAPLEKIIRHCATVGTNTFYSQ----VFPRSKHGKTGSL--
          NA.T.IMIRQL........C.R.ILGL.KDAPLE.IIRHCATVGTNTF.SQ.....F.....G..GS...
Retrocopy NAPTRIMIRQLAREKSS<FCTRVILGLHKDAPLEEIIRHCATVGTNTF*SQAMMQTFQDPNMGRQGSFWQ

Parental  -LARATCQFFQCGKVGHLKAQCWHKIDSGKQDGGPSSRAQSNLVMVVQILTLTV
          ...R.T.Q.FQCGK.GHLKAQCWHK....KQ.G.............VQ.L.L..
Retrocopy RTSRETHQCFQCGKIGHLKAQCWHKGRVKKQGGRTRPKNPMSKMQNVQRLPLRI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_562 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000009835	3 retrocopies	retro_shar_151, retro_shar_195, retro_shar_429,
Sarcophilus harrisii	ENSSHAG00000016712	2 retrocopies	retro_shar_169, retro_shar_562 ,